Nitrogen Metabolism Flashcards
What is an important feature about Amino acids when considering metabolism
Amino acids are not stored in the body for future use
How can Amino acids be obtained?
- The diet
- de novo synthesis
- Recovered from Protein degradation
Catabolism (break-down) of amino acids occurs in two stages what are they
- α-amino group removal through transamination - leaving ammonia which some will be lost in urine
- α-keto acids being converted to metabolic pathway intermediates (CO₂, H₂O, glucose, fatty acids + ketones)
The amino acid pool contains all free amino acids present within an organism (in cell, extracellular fluid, blood plasma)
This pool can have processes which add and take away from it - existing at equilibrium
What processes can add to it
- Amino acids from degraded body proteins (most)
- Amino acids from dietary proteins
- Synthesis of nonesseential amino acids from simple intermediates
What processes can deplete the amino acid pool
- Protein synthesis
- Nitrogen-containing molecule precursors
- Conversion to glucose, glycogen, fatty acids, ketone bodies etc
What enzyme degrades intraceullar proteins
- ATP-dependent ubiquitin-proteasome system
What enzymes degrade extracellular proteins
ATP-independent enzyme system of the lysosome
Proteins selected for degradation are…
Tagged with a molecule of ubiquitin
Occurs at a side chain of lysine, requiring ATP and enzymes to catalyse
Once a protein is ubiquitinated, what does this allow the proteasome to do
Allow cytosolic proteasome to unfold the protein, deubiquitinate it and transports the protein to the proteolytic core
Oligopeptides are formed (protein fragments) which are then acted on by general proteases and amino acids formed enter into the amino acid pool
Degradation of proteins is determined by which structural properties
- Oxidation levels of N-terminal residue
- PEST sequences (serine or aspartate at n-termine as they should be internal AA)
Once dietary proteins are consumed, they enter the stomach where they are broken down
How?
- The stomach excretes gastric juice (with HCL pH 2.5) which will denature proteins
- Pepsin is also produced, which is an endopeptidase, releasing AA and oligopeptides
Once food leaves the stomach, it nexts moves to the pancreas
Here, protein breakdown is said to be more specific, why?
- The pancreas produces proteases which are specific to an amino acids R group
- They are exo- and endoproteases
After the pancreas, food then moves to the small intestine, where…
exopeptidases (aminopeptidase) celave N-terminal residues to produce smaller peptides and AA
What are the ways that free amino acids and Di- and Tri-peptides enter into enterocytes
- Free amino acids are taken into enterocytes by the Na⁺ linked secondary transport system (using ATP to create gradient)
- Di- & Tripeptides are taken up by H⁺ linked transport system, where they are hydrolysed to AA and released into portal system
How do amino acids move into cells
- A concentration gradient exists between the outside of the cell and the inside, where amino acids are actively transported in
- 7 different transport system exist with overlapping specificities for amino acids
What occurs during a transamination reaction, in the breakdown of amino acids
The amino group is transferred to α-Ketoglutarate, forming Glutamate, using the enzyme Aminotraferases
Now we have an α-keto acid
What is the use of Glutamate in the cell once it is formed
Glutamate can be oxidatively deaminated or used as an amino donor group
This can be in non-essential amino acid synthesis
Aminotransferase are found in the liver, kidney and muscle
They are specific for amino group donors, e.g. a aminotransferase which formed alanine would be called…
alanine aminotransferase (ALT)
Aminotransferase are found in the liver, kidney and muscle
They are specific for amino group donors, e.g. a aminotransferase which formed alanine would be called…
alanine aminotransferase (ALT)
What is oxidative deamination
The reaction results in an amino group being released as ammonia from glutamate (which has taken it from the AA)
Occurs in the liver and kindey
Ammonia is then a source of nitrogen in hepatic urea synthesis
What does the enzyme Glutamate dehydrogenase do
This removes the amino group from glutamate and then forms ammonia
Triggered by lots of ADP as AA backbone can be transformed into glucose
Ammonia is highly toxic in the body, it is disposed as
Urea
It forms from an NH₃ from oxidative deamination and one from aspartate, as well as CO₂
This occurs in the liver, where it is transported to kidneys are excreted
The first two reactions of the Urea cycle occur?
In the mitocondrial matrix
The yellow blob
What occurs in the first reaction of the Urea cycle
HCO₂⁻, NH₃, and ATP are used to form carbonyl phosphate by carbonyl phosphate synthase
What occurs in the second reaction of the Urea cycle
An inorganic phosphate is removed from carbonyl phosphate and it is bound to Ornithine creating Citrulline
What happens in the 3rd step of the urea cycle
Citrulline reacts with Aspartate using the enzyme argininosuccinate synthetase and ATP to form Argininosuccinate
What happens in the 4th step of the Urea cycle
Argininosuccinate is acted upon by argininosuccinase, removing fumarate
Arginine then continues on in the Urea cycle and Fumarate will enter other metabolic pathways
Fumerate is a TCA cycle intermediate
How can you form Malate, which is another TCA cycle intermediate
Using Fumarase
From here it will enter the mitocondria and the TCA cycle can continue
What happens in the 5th step of the Urea cycle
Arginine, reacts with Arginase which liberates Urea and forms Ornithine (we are back to the start)
The urea cycle is a very high energy process and irreversible, why?
4 high energy phosphate bonds are consumed
Ammonia is toxic to the ….
High levels lead too
Central nervous system
Hyperammonemia
Where can α-keto acids enter the TCA cycle
Basically anywhere
The entering will result in formation of glucose and lipids as well as energy generation
Catabolism of Glucogenic Amino acids leads to
Yielding pyruvate or TCA cycle intermediates
Basically substrates for gluconeogenesis
What does Catabolism of Ketogenic Amino acids yield
Yields acetoacetate or acetyl Co-A or acetoacetyl Co-A
Carbon skeletons cannot lead to glucose
Why is nitrogen fixation so difficult
due to the strength of the nitrogen triple bond (945kJ mol⁻¹)
Hence nitrogen fixation is comparatively not common
What is the name of the bacteria which can convert N₂ into metabolically useful forms
Diazotrophs
Most well know is rhizobium which form symbotic relationships with plants through root nodules
What happens to the Nitrogen after fixation
Nitrogen is assimilated into biological molecules as amino groups
What enzyme do Diazotrophs use to fix nitrogen
Nitrogenase
This converts N₂ into NH₃
Nitrogen fixation is a very energy rich process, which uses the enzyme nitrogenase, which is a complex of 2 proteins
They are?
- The Fe-protein with ATP binding site
- MoFe-protein
What is a significant feature of nitrogenase
it is rapidly inactivated by O₂
Nitrogen fixation requires an electron source, which they are then transferred to ferrodoxin (4xFe, 4xS) electron carrier
Where do these electrons come from
Generated oxidatively or photosynthetically
Nitrogen fixation requires an electron source, which they are then transferred to ferrodoxin (4xFe, 4xS) electron carrier
Where do these electrons come from
Generated oxidatively or photosynthetically
Once the electron are at ferrodoxin, what happens
through ATP hydrolysis MoFe protein can come closer (conformational change) to ferrodoxin and electrons can move onto it
This changes the MoFe proteins redox potential, allowing N₂ to be reduced
Why is nitrogen fixation a futile cycle
Nitrogen reduction occurs in 3 step, one of which producing diimine, which can react with hydrogen to reform nitrogen
There is also a cost of 16 ATP per N₂ molecule
Not all plants can support nitrogen fixing bacteria
How else can plants obtain nitrogen then?
- Rely on lightening discharges
- Decaying organic matter
- Applied fertilizer
After conversion to biologically useful ammonia, nitrogen must be assimilated into a cell’s biomolecules
How?
Transamination - the movement of an amino group from one molecule to another using aminotransferase
Glutamate (and glutamine for tryptophan & histidine) is important for this
How can you form glutamine from glutamate
Glutamine synthetase can incorporate another ammonium ion into glutamate to form glutamine, driven by ATP
What is the difference between essential and non-esstential amino acids in terms of synthesis
Essential amino acids can only be obtained from the diet - due to complicated synthesis processes
Non-essential can be synthesised by mammals from common intermediates
For nonessential amino acids, many of them come from
glycolytic intermediates which are transaminated
Not only do amino acids act as protein building blocks, they are precursors for…
Nucleotides
Nucleotide co-enzymes
Heme
Hormones
Neurotransmitters
Nucleotides are the phosphate esters of a pentose sugar in which a purine/pyrimidine base is linked
Nucleotides can be synthesised…
de novo: within the cell - the nucleotides are built up from different amino acids
Salvaged: from nucleotides present in the cell
What is the difference between purine and pyrimidine synthesis
Unlike purine synthesis (with pre-exisitng ribose 5-phosphate), pyrimidine ring is synthesised before attachment to ribose-5-phosphate
What is the use of tetrahydrofolate
It acts as a ‘one carbon’ pool
It has carbons in different oxidation states which can be donated for different reactions
What is Methotrexate and it’s affects
An inhibitor known to affect the production of tetrahydrofolate
Through binding to dihydrofolate reductase
affecting ‘one carbon’ pool and affecting pyrimidine/purine synthesis
Henced use to treat cancer
